to bear in mind...

[fabian-paul]

Hi @fnueske I proposed some changes in Pyemma's copy of variational: https://github.com/markovmodel/PyEMMA/pull/1055

[marscher]

Ah the submodule hassle again :+1: But it should be as easy as a git pull from another repository.

[marscher]

On 03/01/2017 03:12 PM, fabian-paul wrote:

Hi @fnueske https://github.com/fnueske I proposed some changes in Pyemma's copy of variational: markovmodel/PyEMMA#1055 https://github.com/markovmodel/PyEMMA/pull/1055

Well, it is (manual) copy paste hassle, because we've decided against submodules.

[fabian-paul]

Well, did we make a decision at all?

[franknoe]

Why copy and paste? I thought we're not using the variational module as a PyEMMA dependency anymore and all that code is in PyEMMA. So the changes should be made in PyEMMA or did I miss something about the variational module?

Am 01/03/17 um 15:18 schrieb Martin K. Scherer:

On 03/01/2017 03:12 PM, fabian-paul wrote:

Hi @fnueske https://github.com/fnueske I proposed some changes in Pyemma's copy of variational: markovmodel/PyEMMA#1055 https://github.com/markovmodel/PyEMMA/pull/1055

Well, it is (manual) copy paste hassle, because we've decided against submodules.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/markovmodel/variational/issues/51#issuecomment-283351614, or mute the thread https://github.com/notifications/unsubscribe-auth/AGMeQpaSH8ih_P33PbqwDysRDvOzl6_Zks5rhX49gaJpZM4MPs7e.

--

---

Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354 Web: research.franknoe.de Mail: Arnimallee 6, 14195 Berlin, Germany

[fabian-paul]

https://github.com/markovmodel/PyEMMA/pull/1055 contains an improvement to variational which could be added to the variational package too, independent of its usefulness for Pyemma.

[fabian-paul]

And in general, I think we should not let variational diverge from the copy of variational that is included in Pyemma. Or was there a contrary decision that I missed?

[franknoe]

I understand, I'm just not sure if we have committed to keep maintaining variational at the moment or just to breed this code within PyEMMA until we think it's ready for an independent package like msmtools. But Feliks knows probably more.

Am 01/03/17 um 15:57 schrieb fabian-paul:

markovmodel/PyEMMA#1055 https://github.com/markovmodel/PyEMMA/pull/1055 contains an improvement to variational which could be added to the variational package too, independent of its usefulness for Pyemma.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/markovmodel/variational/issues/51#issuecomment-283362452, or mute the thread https://github.com/notifications/unsubscribe-auth/AGMeQpxv3SdakWGJ97CtEqkrw7DinA8bks5rhYdWgaJpZM4MPs7e.

--

---

Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354 Web: research.franknoe.de Mail: Arnimallee 6, 14195 Berlin, Germany

[franknoe]

Actually, I thought we had decided to stop maintaining variational until we find that we need it as a package. But again, I may have missed something, so let's see what Feliks says.

Am 01/03/17 um 16:00 schrieb fabian-paul:

And in general, I think we should not let variational diverge from the copy of variational that is included in Pyemma. Or was there a contrary decision that I missed?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/markovmodel/variational/issues/51#issuecomment-283363264, or mute the thread https://github.com/notifications/unsubscribe-auth/AGMeQggbVBEBXn3RJ5Kera7vaTrYl6BFks5rhYgFgaJpZM4MPs7e.

--

---

Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354 Web: research.franknoe.de Mail: Arnimallee 6, 14195 Berlin, Germany

[fnueske]

We didn't make a decision whether or not to continue maintaining variational, so we need to make it now. Can you remind me how the connection between the two is organized right now? Does pyemma use any part of variational now or does it possess its own independent code?

[marscher]

On 02.03.2017 08:51, Feliks Nüske wrote:

We didn't make a decision whether or not to continue maintaining variational, so we need to make it now. Can you remind me how the connection between the two is organized right now? Does pyemma use any part of variational now or does it possess its own independent code?

At the moment pyemma uses its own copy. So there is no need to backport the changes here, if we do not plan to make it a separate package.

[franknoe]

Currently we don't plan to release it separately, so just add a note there that this code is currently not being maintained and people should refer to PyEMMA for that functionality, until further notice.

Am 02/03/17 um 10:24 schrieb Martin K. Scherer:

On 02.03.2017 08:51, Feliks Nüske wrote:

We didn't make a decision whether or not to continue maintaining variational, so we need to make it now. Can you remind me how the connection between the two is organized right now? Does pyemma use any part of variational now or does it possess its own independent code?

At the moment pyemma uses its own copy. So there is no need to backport the changes here, if we do not plan to make it a separate package.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/markovmodel/variational/issues/51#issuecomment-283600941, or mute the thread https://github.com/notifications/unsubscribe-auth/AGMeQt8gNNOmw0fWwQbGdkrI8m9xITh9ks5rhoq5gaJpZM4MPs7e.

--

---

Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354 Web: research.franknoe.de Mail: Arnimallee 6, 14195 Berlin, Germany

[marscher]

Ok